You need to take the Aura Fragment to the Shadow Dimension B4F. When you do that it should be obvious what you have to do. I would suggest obtaining the Light Shard beforehand though, as you will need it to get through the Shadow Dimension. To access the Shadow Dimension, you need to go to either: Sky Pillar, Cave of Destiny, the underground part of the Pokeball place in Krypton City, the former Space Institute in Mossdeep City, or Mt. Moonview. There are more access points, but these are the only ones I remember, and the access point can change, so don't expect to find it and then come back to that spot later and find it there again.